How to operate a motor by a Variable speed drive (VSD) if the motor rated voltage is greater than the VSD supply voltage?

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There is one fact than VSD output voltage can be regulated from zero to the max value that corresponds to VSD input voltage. So if you use 400V supply the max voltage at the VSD output can be 400V.
Different rated frequencies in input (supply) and output (motor) voltage do not play a role at all. The input AC circuit and output AC circuit are separated by DC bus, so no matter the difference in frequency.
Speaking about the VSD output voltage, the limited output voltage does not necessarily mean a problem. Everything depends on the speed operating range and load.
As you know, the torque in the motor is build when the motor is magnetized (flux exists). The rated torque in the motor can be achieved when the motor has rated flux which means that as far as we can respect u/f = constant, the motor will have rated flux.
For example, if the motor rated voltage is 440V, 60Hz, the rated constant u/f = 440V / 60 Hz can be kept up to the limit of supply voltage 400V and that is 440/60=400/f_limit
Hence f_limit gives you 54.5 Hz
As a result, if the drive is supplied by 400V, 50Hz and so the max voltage at the output is 400V then your 460V/60Hz motor will get rated torque up to 54.5Hz. If you go over this speed, the motor will work in the field-weakening area (the motor will gradually lose the torque). If you do not need 100% of the torque (depending on the application) then you can even operate the motor in the field-weakening area.

Summary

Using 400V supply, surely no problem to operate 440V/60Hz motor up to 54.5Hz. Rated torque in the motor can be built continuously, without getting drive or motor overloaded.
Over 54.5Hz, everything depends on the torque required by the load. The torque in the motor will be lowered, at 60Hz the max continuous torque will be approx. 80% of rated torque. It can be enough for the loads that do not require more than 80% of the motor-rated torque. If the load requires more torque, then the only solution is to arrange higher supply voltage at VSD input, e.g. transformer 400V/460V upstream the VSD